The Philippines is considered one of the most vulnerable and susceptible countries to the effects of natural disasters due to its location. Therefore, the country needs to be resilient to the natural calamities it faces yearly. The research aimed to determine the factors that affect the protective behavior of Filipinos during natural disasters by integrating protective motivation theory, the theory of planned behaviors, and ergonomic appraisals, and by adding variables such as knowledge and geographical perspectives. PLS-SEM was used to determine the significant factors that affect protective behavior. A questionnaire was developed and distributed to 302 Filipinos in the Philippines through a digital survey using Google forms. The analysis showed that the intention to prepare is the most significant factor affecting their protective behavior, followed by macro and physical ergonomics. Aside from this, attitudes, perceived severity, self-efficacy, response efficacy, response cost, and subjective norms were found to influence their intention to prepare significantly. Furthermore, understanding natural calamities significantly influences an individual’s perceived severity. However, the geographical perspective, perceived vulnerability, perceived behavioral control, and cognitive ergonomics were found to have an insignificant influence on protective behavior for natural calamities. The study findings could be used as a basis for household units or the national government to build disaster management plans and resilience programs. Aside from this, it can also be used by researchers as a basis for exploring other areas that may affect the protective behavior of individuals to prepare for natural calamities worldwide.